Table 8.
Summary of final results for the PharmaBench based on random split.
| Property | Metrices | RF | XGBoost | CMPNN | FPGNN | DHTNN | KANO | MPG | Unimol | Trans-M |
|---|---|---|---|---|---|---|---|---|---|---|
| LogD | R | 0.573 | 0.786 | 0.86 | 0.865 | 0.801 | 0.898 | 0.888 | 0.901 | 0.901 |
| MAE | 0.866 | 0.618 | 0.528 | 0.489 | 0.613 | 0.434 | 0.464 | 0.452 | 0.431 | |
| RMSE | 1.14 | 0.868 | 0.757 | 0.715 | 0.844 | 0.631 | 0.672 | 0.671 | 0.639 | |
| Solubility | R | 0.49 | 0.629 | 0.645 | 0.706 | 0.547 | 0.703 | 0.699 | 0.723 | 0.612 |
| MAE | 0.711 | 0.592 | 0.619 | 0.536 | 0.658 | 0.54 | 0.545 | 0.516 | 0.635 | |
| RMSE | 0.871 | 0.76 | 0.801 | 0.712 | 0.838 | 0.712 | 0.72 | 0.695 | 0.812 | |
| PPB | R | 0.389 | 0.581 | 0.411 | 0.705 | 0.236 | 0.655 | 0.705 | 0.697 | 0.719 |
| MAE | 0.14 | 0.122 | 0.15 | 0.103 | 0.19 | 0.111 | 0.101 | 0.111 | 0.106 | |
| RMSE | 0.202 | 0.19 | 0.273 | 0.168 | 0.257 | 0.189 | 0.191 | 0.208 | 0.2 | |
| CYP 3A4 | R | 0.247 | 0.467 | 0.368 | 0.609 | 0.387 | 0.485 | 0.584 | 0.593 | 0.564 |
| MAE | 10.977 | 9.761 | 9.865 | 7.892 | 10.744 | 10.033 | 8.33 | 8.545 | 8.536 | |
| RMSE | 18.374 | 17.565 | 19.903 | 15.735 | 17.324 | 17.036 | 16.128 | 16.842 | 16.619 | |
| CYP 2C9 | R | 0.073 | 0.141 | 0.148 | 0.251 | 0.19 | 0.154 | 0.388 | 0.29 | 0.332 |
| MAE | 10.823 | 10.62 | 8.733 | 9.746 | 10.503 | 9.858 | 8.518 | 8.567 | 8.882 | |
| RMSE | 17.08 | 16.959 | 17.849 | 16.419 | 16.864 | 16.916 | 16.788 | 17.9 | 16.174 | |
| CYP 2D6 | R | 0.213 | 0.232 | 0.328 | 0.477 | 0.278 | 0.498 | 0.527 | 0.47 | 0.463 |
| MAE | 12.129 | 13.097 | 10.802 | 10.999 | 13.251 | 10.697 | 10.196 | 10.227 | 10.927 | |
| RMSE | 19.826 | 20.685 | 21.612 | 19.948 | 20.467 | 19.385 | 20.012 | 20.695 | 20.664 | |
| HLMC | R | 0.462 | 0.652 | 0.223 | 0.712 | 0.497 | 0.684 | 0.738 | 0.538 | 0.705 |
| MAE | 0.521 | 0.427 | 0.707 | 0.419 | 0.576 | 0.465 | 0.41 | 0.604 | 0.442 | |
| RMSE | 0.697 | 0.605 | 1.008 | 0.628 | 0.789 | 0.668 | 0.599 | 0.862 | 0.631 | |
| RLMC | R | 0.492 | 0.675 | 0.363 | 0.704 | 0.564 | 0.738 | 0.753 | 0.683 | 0.721 |
| MAE | 0.511 | 0.395 | 0.589 | 0.378 | 0.494 | 0.376 | 0.357 | 0.426 | 0.381 | |
| RMSE | 0.692 | 0.557 | 0.867 | 0.52 | 0.683 | 0.514 | 0.495 | 0.609 | 0.543 | |
| MLMC | R | 0.621 | 0.766 | 0.349 | 0.811 | 0.6 | 0.785 | 0.8 | 0.738 | 0.772 |
| MAE | 0.628 | 0.447 | 0.765 | 0.409 | 0.629 | 0.45 | 0.414 | 0.521 | 0.428 | |
| RMSE | 0.862 | 0.62 | 1.106 | 0.567 | 0.863 | 0.633 | 0.569 | 0.747 | 0.59 | |
| BBB | ACC | 0.796 | 0.81 | 0.842 | 0.852 | 0.842 | 0.867 | 0.865 | 0.861 | 0.847 |
| AUC | 0.698 | 0.726 | 0.901 | 0.93 | 0.903 | 0.934 | 0.925 | 0.918 | 0.922 | |
| F1 | 0.867 | 0.873 | 0.814 | 0.886 | 0.882 | 0.907 | 0.849 | 0.842 | 0.829 | |
| AMES | ACC | 0.726 | 0.791 | 0.78 | 0.79 | 0.751 | 0.795 | 0.807 | 0.788 | 0.803 |
| AUC | 0.727 | 0.791 | 0.847 | 0.87 | 0.83 | 0.869 | 0.879 | 0.857 | 0.88 | |
| F1 | 0.715 | 0.788 | 0.78 | 0.782 | 0.756 | 0.8 | 0.807 | 0.787 | 0.802 |